9NZN
Crystal Structure of Kirsten Rat Sarcoma G12C Complexed with GDP and Covalently Bound to an Adduct of (2S)-1-{4-[(7P)-7-(8-ethynyl-7-fluoro-3-hydroxynaphthalen-1-yl)-8-fluoro-2-{[(2R,4R,7aS)-2-fluorotetrahydro-1H-pyrrolizin-7a(5H)-yl]methoxy}pyrido[4,3-d]pyrimidin-4-yl]piperazin-1-yl}-2-fluoro-3-(1,3-thiazol-2-yl)propan-1-one
This is a non-PDB format compatible entry.
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | NSLS-II BEAMLINE 17-ID-1 |
| Synchrotron site | NSLS-II |
| Beamline | 17-ID-1 |
| Temperature [K] | 100 |
| Detector technology | PIXEL |
| Collection date | 2023-01-29 |
| Detector | DECTRIS EIGER X 9M |
| Wavelength(s) | 0.92000 |
| Spacegroup name | P 21 21 21 |
| Unit cell lengths | 40.095, 50.928, 90.182 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 17.480 - 1.504 |
| R-factor | 0.2064 |
| Rwork | 0.205 |
| R-free | 0.22420 |
| Structure solution method | MOLECULAR REPLACEMENT |
| RMSD bond length | 0.010 |
| RMSD bond angle | 1.030 |
| Data reduction software | XDS (Jan 10, 2022) |
| Data scaling software | Aimless (0.7.8) |
| Phasing software | AMoRE |
| Refinement software | BUSTER (2.11.8) |
Data quality characteristics
| Overall | Inner shell | Outer shell | |
| Low resolution limit [Å] | 45.091 | 45.091 | 1.591 |
| High resolution limit [Å] | 1.504 | 4.430 | 1.504 |
| Rmerge | 0.082 | 0.052 | 0.989 |
| Rmeas | 0.086 | 0.055 | 1.100 |
| Rpim | 0.024 | 0.015 | 0.466 |
| Total number of observations | 294191 | 15997 | 6895 |
| Number of reflections | 25968 | 1298 | 1299 |
| <I/σ(I)> | 14.92 | 39.89 | 1.34 |
| Completeness [%] | 91.8 | 99.8 | 43.9 |
| Completeness (spherical) [%] | 86.4 | 99.8 | 28.5 |
| Completeness (ellipsoidal) [%] | 91.8 | 99.8 | 43.9 |
| Redundancy | 11.33 | 12.32 | 5.31 |
| CC(1/2) | 0.999 | 0.998 | 0.521 |
| Anomalous completeness (spherical) | 86.3 | 100.0 | 30.2 |
| Anomalous completeness | 91.9 | 100.0 | 45.9 |
| Anomalous redundancy | 6.0 | 7.3 | 2.7 |
| CC(ano) | -0.100 | -0.075 | -0.076 |
| |DANO|/σ(DANO) | 0.7 | 0.8 | 0.6 |
| Diffraction limits | Principal axes of ellipsoid fitted to diffraction cut-off surface |
| 1.504 Å | 1.000, 1.000, 1.000 |
| 1.530 Å | 0.000, 0.000, 0.000 |
| 1.584 Å | 0.000, 0.000, 0.000 |
| Criteria used in determination of diffraction limits | local <I/sigmaI> ≥ 1.2 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 4.6 | 277 | 100 MM Sodium acetate anhydrous, pH 4.6, 200 MM ammonium sulfate, 25% (w/v) PEG 4000 |
